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Catalytic fragment of cholix toxin from vibrio cholerae in complex with inhibitor V30
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q6M PDB entry 2Q6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 15% PEG-8000, 0.02 M KH2PO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.489 α = 90 b = 64.973 β = 90 c = 86.603 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm Multilayer mirror, curved to focus in the vertical (R = 400 m) 2010-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.03796 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.68 30 99.8 0.058 19.59 5.6 23603 23558 -3 23.237
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.68 1.72 99.9 0.523 3.7 5.4 1695
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2Q6M 1.68 29.31 23557 23557 1178 100 0.176 0.174 0.1936 0.2 0.2164 RANDOM 17.342
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.332 r_dihedral_angle_4_deg 16.869 r_dihedral_angle_3_deg 13.44 r_dihedral_angle_1_deg 5.797 r_scangle_it 3.032 r_scbond_it 1.869 r_angle_refined_deg 1.363 r_mcangle_it 1.061 r_mcbond_it 0.622 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.332 r_dihedral_angle_4_deg 16.869 r_dihedral_angle_3_deg 13.44 r_dihedral_angle_1_deg 5.797 r_scangle_it 3.032 r_scbond_it 1.869 r_angle_refined_deg 1.363 r_mcangle_it 1.061 r_mcbond_it 0.622 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1547 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 37
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction